Part 2 of the analysis. Continued directly from KP_model_data_filtering_part1.ipynb.

Cleanup of each lineage separately

Fibroblast

PCA, tSNE, Clusters on Fibroblasts

Clean the fibroblast data

Re-do PCA, tSNE, Clusters

Fibroblast cell type annotation

Endothelial

PCA, tSNE, Clusters on Endothelials

Cleanup endothelial sub-population

Re-do PCA, tSNE, Clusters

Cell type annotation

Endomarkers

Immgenes

Please see KP_model_data_filtering_part3.ipynb for rest of the analysis (Myeloid lineage).